Variant report

Variant	rs33544
Chromosome Location	chr5:112321070-112321071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:112320458-112323245	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112312385..112315007-chr5:112318753..112321264,2	MCF-7	breast:

Variant related genes	Relation type
DCP2	TF binding region
ENSG00000172795	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1057474	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs12654474	0.86[ASN][1000 genomes]
rs13156493	0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs13171553	0.84[ASN][1000 genomes]
rs13176362	0.80[ASN][1000 genomes]
rs13177101	0.85[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs13186334	0.85[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs13445	0.85[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap]
rs1363333	0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs1549181	0.90[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs1549182	0.89[ASN][1000 genomes]
rs17312754	0.86[ASN][1000 genomes]
rs17372511	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2112454	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.95[ASN][1000 genomes]
rs2416300	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs3185733	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs33545	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33548	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33549	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs33551	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs33552	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs33554	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33558	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33559	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33560	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33561	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33566	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs33568	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs33569	0.80[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs3857434	0.90[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4075350	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs4705529	0.90[ASN][1000 genomes]
rs4705744	0.87[ASN][1000 genomes]
rs4705749	0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs4705750	0.90[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs4705752	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4778	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7670	0.85[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs7701781	0.90[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs7733863	0.86[ASN][1000 genomes]
rs9122	0.90[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs9784647	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1028759	chr5:112300490-112358514	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs33544	MCC	cis	cerebellum	SCAN
rs33544	DCP2	cis	multi-tissue	Pritchard
rs33544	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs33544	DCP2	Cis_1M	lymphoblastoid	RTeQTL
rs33544	TSLP	cis	parietal	SCAN
rs33544	MCC	cis	Whole Blood	GTEx
rs33544	DCP2	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112313200-112329000	Weak transcription	Spleen	Spleen
2	chr5:112313800-112337600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:112314000-112329000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:112314000-112335400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:112314000-112337200	Weak transcription	Lung	lung
6	chr5:112314000-112338200	Weak transcription	Gastric	stomach
7	chr5:112314200-112326800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:112314200-112328800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:112314200-112328800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:112314200-112332000	Weak transcription	Fetal Kidney	kidney
11	chr5:112314200-112332000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:112314200-112337000	Weak transcription	HSMMtube	muscle
13	chr5:112314200-112338200	Weak transcription	Aorta	Aorta
14	chr5:112314200-112341000	Weak transcription	Small Intestine	intestine
15	chr5:112314200-112349600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:112314200-112356800	Weak transcription	Stomach Mucosa	stomach
17	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
18	chr5:112314400-112322400	Weak transcription	Thymus	Thymus
19	chr5:112314400-112338400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr5:112314800-112322400	Weak transcription	Liver	Liver
21	chr5:112314800-112324400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr5:112314800-112324400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:112314800-112325800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:112314800-112332000	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:112314800-112332000	Weak transcription	NHLF	lung
26	chr5:112314800-112332200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:112314800-112337200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:112314800-112349200	Weak transcription	Brain Substantia Nigra	brain
29	chr5:112315400-112330800	Weak transcription	Brain Anterior Caudate	brain
30	chr5:112315600-112328600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:112315600-112332000	Weak transcription	NHDF-Ad	bronchial
32	chr5:112315600-112332200	Weak transcription	Ovary	ovary
33	chr5:112315600-112339400	Weak transcription	Hela-S3	cervix
34	chr5:112315600-112362600	Weak transcription	Brain Angular Gyrus	brain
35	chr5:112315800-112329200	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:112315800-112334600	Weak transcription	Brain Germinal Matrix	brain
37	chr5:112316000-112332200	Weak transcription	Fetal Brain Female	brain
38	chr5:112316000-112337000	Weak transcription	A549	lung
39	chr5:112316200-112324600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:112316400-112324200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:112316400-112330000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:112316600-112326600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:112316600-112330000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr5:112316800-112326200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:112317000-112332000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:112317000-112338200	Weak transcription	Left Ventricle	heart
47	chr5:112317400-112322200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr5:112317800-112322000	Weak transcription	Fetal Intestine Large	intestine
49	chr5:112317800-112322000	Weak transcription	Fetal Intestine Small	intestine
50	chr5:112317800-112322000	Weak transcription	Fetal Stomach	stomach

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